ok, the reason that your camera is doing this is because of its light metering system
oftentimes your camera exposes the shot so that your subject is properly exposed, while the sky is blown out and overexposed, because you need either a smaller aperture or faster shutter speed to expose the sky properly (the point being less light), which would, unaided, underexpose your subject
generally what you need to do to fix this is expose your camera for the sky (either point it straight up at the sky and take an exposure reading and lock the exposure, or switch to manual mode and punch in those settings) then compose your shot as you would, but add a flash
the flash fills in the subject, (usually) properly exposing them, and because your exposing for the sky, that doesnt blow out
hope you got that hahah
others can probably explain it better than me =P

My guess (and it really is a guess) is that it also has to do with the position of the sun relative to your subject. It is probably somewhere behind you coming over your shoulder in the first one so it adequately lights both the clouds and the front of the building. It is my bet that it is somewhere behind the buildings in front of you in the second and third images, so the front of the buildings are in shadow -- making it hard to get the sky and the building front both with adequate exposure (unless you do an HDR).

On the first one, the sun is shining from the left hand side, illuminating most of the buildings and giving a sky which does not differ too much from the buildings in brightness. Hence your camera is able to capture both of them well exposed.

In the second and third image, the sun must have been in a different location - probably in front of you to the right. Therefore the building gets hardly any light, but the sky is bright. A digital camera often cannot really capture this range of brightness, hence you get either the building exposed well and the sky overexposed, or you get the sky exposed right and the building underexposed.

With your metering and all on auto, the camera makes this decision, depending on where exactly you point it.

As Alex_B mentioned, because of your orientation to the sun (based on the shadows, it seems to be off to the left) the foreground and sky are lit more evenly. Your orientation to the sun is also the reason the sky is a deep blue with the polarizer. Polarization of the sky is strongest at 90 degrees perpendicular to the sun. As your lens moves toward the sun or 180 degrees from it, the effect weakens.

Also, your polarizer has a rotating ring that allows you to increase or decrease the overall effect. I noticed that each photo is at a different focal length. As someone else mentioned, if your lens's filter mount rotates when you focus or zoom the effect will change because the filter is rotating as well. If this is the case, readjust the polarizer after you are satisfied with the zoom and focus.